Contacts of the strand formed by residues 334 - 342 (chain E) in PDB entry 2W3S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 334 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193E TYR* 2.9 15.8 + - - -
307E LEU* 3.7 23.9 - - + +
308E ARG 3.8 5.2 + - - -
309E ARG* 3.6 28.8 + - + +
312E GLU 6.0 0.3 - - - -
314E ARG* 2.5 49.0 + - - +
330E ARG* 3.1 26.1 + - + +
331E ARG* 3.0 36.4 + - - +
332E PRO 3.2 1.4 + - - -
333E GLY* 1.3 78.6 - - - +
335E PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E SER* 4.6 4.9 - - - -
189E LEU* 3.9 27.1 - - + -
190E ALA* 3.6 39.0 - - + -
193E TYR* 3.8 24.7 - + + -
201E LEU* 4.1 4.9 - - + -
231E LEU* 4.7 5.6 - - + -
307E LEU* 3.8 4.9 - - - -
308E ARG* 3.0 67.3 + - + -
310E GLY 4.7 1.1 - - - -
330E ARG* 4.1 1.3 - - - +
333E GLY 4.5 2.7 - - - -
334E GLU* 1.3 75.5 - - - +
336E VAL* 1.3 72.8 + - - +
337E GLU* 3.3 24.8 + - + -
1465E FAD 3.5 17.7 - - + +
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Residues in contact with VAL 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E LEU* 4.3 0.5 - - - +
245E ALA* 3.1 17.0 - - + +
282E GLY* 4.3 13.7 - - - +
285E ILE* 4.8 5.6 - - + -
286E ALA* 3.8 21.3 - - + +
305E LEU* 3.6 25.8 - - + -
306E THR 4.2 3.1 - - - -
307E LEU* 4.2 16.6 - - + -
321E PHE* 4.5 11.2 - - + -
330E ARG* 4.7 2.9 - - - +
335E PHE* 1.3 74.8 - - - +
337E GLU* 1.3 60.3 + - - +
338E SER* 4.6 3.1 - - - +
339E VAL* 5.8 0.2 - - + -
1465E FAD 2.9 44.6 + - + +
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Residues in contact with GLU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E SER* 4.0 8.8 + - - +
231E LEU* 3.1 20.6 - - + +
244E GLY* 3.8 1.2 - - - -
245E ALA* 3.0 18.1 + - - -
306E THR* 3.0 20.0 + - + +
308E ARG* 3.4 45.8 + - + +
313E ARG* 3.5 31.1 + - - +
335E PHE* 3.3 22.8 + - + -
336E VAL* 1.3 74.3 - - - +
338E SER* 1.3 69.9 + - - +
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Residues in contact with SER 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E GLY* 5.6 0.9 - - - -
243E ILE 3.1 19.2 + - - -
244E GLY* 3.7 7.0 - - - -
245E ALA* 3.7 7.6 - - - +
305E LEU* 3.7 6.6 - - - +
306E THR* 2.8 46.5 + - - +
336E VAL* 3.9 1.2 - - - +
337E GLU* 1.3 86.9 + - - +
339E VAL* 1.3 63.0 + - - +
340E THR* 4.7 3.1 + - - -
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Residues in contact with VAL 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E GLY 3.6 0.2 - - - -
243E ILE* 2.6 64.3 + - + +
252E LEU* 6.5 0.2 - - + -
281E ILE* 4.9 9.4 - - + -
285E ILE* 3.6 30.7 - - + -
298E LEU* 4.3 12.6 - - + -
303E ALA* 5.8 0.4 - - + -
304E SER 3.2 14.8 - - - +
305E LEU* 3.8 13.9 - - + -
306E THR* 5.1 0.4 - - - -
318E LEU* 4.9 2.7 - - + -
336E VAL* 5.8 0.4 - - + -
338E SER* 1.3 78.6 + - - +
340E THR* 1.3 62.2 + - - +
341E LEU* 4.4 15.3 - - + -
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Residues in contact with THR 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E THR* 3.9 8.1 - - + +
239E ASP* 3.6 24.2 - - - +
240E GLY* 3.9 0.4 - - - -
241E TYR 3.0 26.9 - - - +
242E GLY* 3.8 7.0 - - - +
303E ALA* 3.4 3.1 - - - +
304E SER* 2.9 44.2 + - - -
306E THR* 4.8 5.9 + - - -
315E ARG* 5.4 6.2 + - - +
338E SER* 4.7 4.9 + - - -
339E VAL* 1.3 78.0 + - - +
341E LEU* 1.3 68.1 + - - +
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Residues in contact with LEU 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E GLY* 3.0 5.5 - - - -
241E TYR* 2.7 33.8 + - + +
243E ILE* 3.4 31.4 - - + -
252E LEU* 5.0 2.5 - - + -
255E PHE* 5.1 4.9 - - + -
260E HIS* 4.6 11.7 - - + -
263E LEU* 4.5 9.4 - - + -
298E LEU* 3.8 24.7 - - + -
301E MET* 3.8 29.8 - - + -
303E ALA* 3.7 17.7 - - + -
339E VAL* 4.4 7.4 - - + -
340E THR* 1.3 82.3 - - - +
342E PRO* 1.4 73.3 - - + +
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Residues in contact with PRO 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E ASP 4.2 4.9 - - - +
240E GLY* 3.9 4.9 - - - -
241E TYR* 3.9 3.6 - - - -
260E HIS* 2.8 26.8 + - + -
301E MET* 3.2 36.1 - - + +
302E GLY 4.6 3.4 - - - +
303E ALA* 4.6 6.1 - - - -
341E LEU* 1.4 92.0 - - + +
343E LYS* 1.3 59.9 + - - +
344E SER 3.8 19.3 - - - +
345E ALA* 4.7 1.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il